{ version = 2.59; (* of makebk.p 2005 Feb 7}
(* begin module describe.makebk *)
(*
name
makebk: make a book from a file of sequences.
synopsis
makebk(sequ: in, book: out, changes: out, output: out, input: intty)
files
sequ: file of raw sequences, each ending in a '.'; no characters are
allowed in this file except the bases (a,c,g,t,u) and period and blank.
Characters other than these will be converted to 'a' and the change
will be noted in the changes file. The bases can also be in capital
letters.
book: the output file containing the sequences and the necessary
information for it to be a proper book. the user types in the
required information after prompts from the program.
changes: Delila programs cannot handle sequences that have ambiguities
because Delila was designed on the assumption that people would
finish their sequences. Unfortunately this is not true, and the
databases contain bases other than acgt to indicate ambiguity.
These are converted to "a" and the cases are reported in this file.
NOTE: "u" is converted to "t".
output: for messages and queries to the user
input: interactive input.
Type a carriage return to start; this is (unfortunately) ignored.
Then the program asks:
Is this an insertion module (m), an independent book (b),
or an automatically generated book (a, z), using default values?
Chose the kind of output you want. An 'a' will give you an
automatically generated book, while 'z' will do the same but it will
first ask you which base is to be the zero coordinate of each
sequence. This allows one to shift the alignment.
If you do not chose the automatic route, you will be prompted
for all the parts of the book.
New as of 2005 Feb 7:
In the automatic route, names of pieces may follow the title.
On each line:
The key name is given.
a space is given
the rest of the line is the long name.
description
Makebk takes a file of raw sequences (sequ) separated by periods (.)
and converts that into a proper delila book format, getting the
required information from the user. The user may also have makebk fill
in the piece information automatically, using default values.
see also
Another program to convert a single sequence to a Delila book: rawbk.p
A program to list the contents of your new book: lister.p
This program evolved as an interactive one, but can be used
under Unix as if it had a parameter file. To do this, execute it
in this form:
makebk < makebkp
where makebkp is an example parameter file that will read
all sequences and give a simple title. It consists of three or
more lines:
this line is ignored.
a this line triggers automatic book generation
title This is the title
name1 first sequence name
name2 second sequence name
author
Gary Stormo
bugs
The delila system requires complete sequence. To handle sequences
with unknown bases, they are replaced with constant chreplace.
technical notes
The constant chreplace replaces all unidentified characters in the
sequence.
*)
(* end module describe.makebk *)
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